Molecular characterization of Hawaiian Sugarcane yellow leaf virus genotypes and their phylogenetic relationship to strains from other sugarcane-growing countries

Abstract

Sugarcane yellow leaf virus (SCYLV) is the causal agent of the sugarcane disease Yellow leaf (YL), which was first reported in Hawaii. The presence of SCYLV was detected by tissue blot immunoassay and the Hawaiian sugarcane cultivars fell into susceptible cultivars (with SCYLV) and resistant cultivars (without SCYLV). RT-PCR showed recently that the resistant cultivars also contain the virus, however with a 100-fold lower virus titre than in the susceptible cultivars. SCYLV is present as whole genome (6 kb) or as two subgenomic sequences of 2.4 and 1.0 kb. Virus preparations from three Hawaiian cultivars (one resistant and two susceptible) were fully sequenced and the sequences were aligned to published, full and partial sequences. The phylograms corroborate previous findings that the so-called YLS-segment, which codes for the coat protein, shows the least genetic diversity, whereas the other sequence fragments A-D, representing the ORFs 0-5, expressed a two-fold higher diversity. The Hawaiian SCYLV-strains clustered together next to the Peru strain, apart from the BRA-strains and well apart from the REU-strains. We propose that the Hawaiian SCYLV should be considered as an independent group together with the Peru strain and known as HAW-PER. The sequences from the two susceptible cultivars had a deletion of 48 to 54 nt in ORF1, which codes for the gene silencing suppressor and a RNA-dependent RNApolymerase. It is speculated that this deletion is important for the high proliferation rate of the virus in the susceptible plants.

Molecular detection, genetic diversity and distribution of Sugarcane yellow leaf virus genotypes in China

“…It is well known that the topology of a SCYLV phylogenetic tree will be slightly varied depending on the targeted region (gene or the whole genome) (ElSayed et al 2011;Lin et al 2014). This difference in clustering could be due to the fact that the SCYLV genes used for phylogenetic analysis have experienced different evolutionary histories (Lin et al 2014).…”

“…Among these ORFs, ORF0 encodes the P0 protein, which is an RNA-silencing suppressor and plays roles in viral pathogenicity and the expression of disease symptoms after infection (Mangwende et al 2009). So far, at least 10 SCYLV genotypes have been reported based on phylogenetic analysis at full genome or individual gene levels and geographic origins: BRA (from Brazil), PER (from Peru), CUB (from Cuba), REU (from Réunion Island), HAW (from Hawaii), COL (from Colombia), IND (from India), CHN1, CHN2, and CHN3 (from China) (Abu Ahmad et al 2006a, b;ElSayed et al 2011;Moonan and Mirkov 2002;Gao et al 2012;Chinnaraja et al 2013;Wang and Zhou 2010;Wang et al 2012;Lin et al 2014). SCYLV genotypes from different geographical locations may have highly heterogeneous sequences at genome level (Lin et al 2014) and distinguishing virulence characteristics by aphid transmission assays (Abu Ahmad et al 2007).…”

“…SCYLV genotypes from different geographical locations may have highly heterogeneous sequences at genome level (Lin et al 2014) and distinguishing virulence characteristics by aphid transmission assays (Abu Ahmad et al 2007). However, genotypes BRA, PER, and HAW share a high level of identify and tend to be grouped into BRA-PER and HAW-PER (Abu Ahmad et al 2006b;ElSayed et al 2011). BRA is the most widespread genotype throughout the world (Abu Ahmad et al 2006a;Gao et al 2012;Lin et al 2014).…”

Investigation of ORF0 as a sensitive alternative diagnostic segment to detect Sugarcane yellow leaf virus

“…In addition, the so-called resistant cultivars (H78-4153 and H78-7750), which previously were thought to be virus-free based on a tissue blot immunoassay (TBIA) (Schenck and Lehrer 2000), also contained the virus. Obviously, the immunological assay is less sensitive than RT-PCR, and only the cultivar line that was generated by meristem tip culture was indeed virus-free (ElSayed et al 2011). The ORF0 fragment was amplified in all SCYLV-preparations and revealed high virus titers.…”

“…The deduced amino acid sequence of P0 proteins is highly conserved among different geographic isolates of SCYLV (Abu Ahmad et al 2006;ElSayed et al 2011). However, the amino acid sequence identity between the P0s of poleroviruses is very low.…”